Research workbench
Crystal structure of the 2H-phosphatase domain of sts-2 in complex with phosphate
Analyse Crystal structure of the 2H-phosphatase domain of sts-2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DB1
- Type
- protein
- Length
- 1,059 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sts-2 protein
- UniProt
- Q8BX41
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sts-2 protein | protein | 267 | 35% helix, 15% strand | Q8BX41 |
| B | Sts-2 protein | protein | 263 | 33% helix, 15% strand | Q8BX41 |
| C | Sts-2 protein | protein | 264 | 34% helix, 15% strand | Q8BX41 |
| D | Sts-2 protein | protein | 265 | 35% helix, 15% strand | Q8BX41 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.81 | 0.85 | 61 | PO4 |
| 2 | 123 | 0.68 | 0.90 | 20 | empty |
| 3 | 324 | 0.67 | 0.81 | 38 | empty |
| 4 | 285 | 0.65 | 0.81 | 37 | empty |
| 5 | 454 | 0.64 | 0.77 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2374 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 2324 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 1118 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 424 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 144 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3DB1 · Crystal structure of the 2H-phosphatase domain of Sts-2 in complex with phosphate · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8BX41
- Elsewhere: RCSB PDB 3DB1 · PDBe 3DB1 · UniProt Q8BX41
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